If your 520 chain or sprocket flies off and cracks your cases or breaks something on a new bike...thats not a factory part that caused the damage, so in theroy, no, anything that happens to the bike due to that part (non-Yamaha), isn't covered under warranty. If it's installed properly you never have to worry about it being a problem. Installing any aftermarket part cannot and never will automatically void your full warranty on anything.
